4Pipe4rc

##CoBiG² 4Pipe4 configuration file
##Lines that begin with a "#" are comments and they are not read
##by the program. They are used only to describe the options.

##The pipeline requires access to several programs which can
##differ from system to system. Here is where we steup the paths
##to each of the required programs.

#Please use the FULL PROGRAM PATHS!
#eg. "/home/user/software/sff_extract" instead of "~/software/sff_extract"

[Program paths]
#Path to seqclean:
seqclean_path =
#Path to cln2qual:
cln2qual_path =
#Path to univec database (file of filenames):
UniVecDB_path =
#Path to mira:
mira_path =
#Path to EMBOSS getorf:
GetORF_path =
#Path to EMBOSS etandem:
Etandem_path =
#Path to BLAST (works with blast2 and blastx):
BLAST_path =
#Path to BLAST database (file of filenames):
BLASTdb_path =
#Path to Blast2go4pipe:
Blast2go_path =
#Path to 4Pipe4's templates directory:
Templates_path =
#Path to 7zip:
7z_path =

[Variables]
#Maximum percent of reads allowed so start with the same bases:
max_equality = 40
#Minimum length of sequences not to be discarded by seqclean:
min_len = 50
#Number of CPU cores to be used by seqclean, BLAST and mira:
seqcores = 10
#Minumim base coverage to accept as a putative SNP:
mincov = 15 # 20 or 25 are better suited for illumina data
#Minimum average base quality to accept as a putative SNP:
minqual = 70 # 60 will suffice for illumina data
#Minimum contig quality to accept SSR:
min_ssr_qual = 70

[Mira Parameters]
##Parameters to put inside mira's manifest file':
##Example to search for SNPs in EST data:

#mirajob = job = est,denovo,accurate
#miracommon = parameters = COMMON_SETTINGS -AS:nop=5:ugpf=off -CO:mr=on:asir=on -OUT:output_result_caf=off:output_result_maf=on
#mira454 = 454_SETTINGS -AL:egp=off -CL:cpat=on
#mirasolexa = SOLEXA_SETTINGS -CO:asir=yes AL:egp=off
#mirareadgroup = readgroup = Test data
#miratech = technology = 454

mirajob =
miracommon =
mira454 =
mirasolexa = 
mirareadgroup =
miratech =